Research workbench
Structure of SARS-cov-2 3CL protease in complex with inhibitor 1C
Analyse Structure of SARS-cov-2 3CL protease in complex with inhibitor 1C in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LZX
- Type
- protein
- Length
- 601 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3C-like proteinase
- EC
- 3.4.22.69
- UniProt
- P0DTD1
- Ligands
- YMG, YMD
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3C-like proteinase (EC 3.4.22.69) | protein | 299 | 25% helix, 29% strand | P0DTD1 |
| B | 3C-like proteinase (EC 3.4.22.69) | protein | 302 | 26% helix, 29% strand | P0DTD1 |
Ligands and binding sites
- YMG · (1S,2S)-2-((S)-2-((((4,4-dimethylcyclohexyl)oxy) carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- YMD · (1R,2S)-2-((S)-2-((((4,4-dimethylcyclohexyl)oxy) carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid · ligand · 2 copies · chains A, B
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1066 | 0.75 | 0.78 | 96 | empty |
| 2 | 216 | 0.57 | 0.79 | 42 | empty |
| 3 | 205 | 0.52 | 0.77 | 28 | YMG, YMD |
| 4 | 169 | 0.51 | 0.78 | 24 | YMG, YMD |
| 5 | 79 | 0.34 | 0.75 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 970 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 7LZX · Structure of SARS-CoV-2 3CL protease in complex with inhibitor 1c · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTD1
- Elsewhere: RCSB PDB 7LZX · PDBe 7LZX · UniProt P0DTD1
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